title: Folding Keratin Gene Clusters During Skin Specification

status: Public on Jun 08 2020

city: Los Angeles

first: Ya-Chen

last: Liang

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

summary: Regional specification is critical for skin development, regeneration and evolution. The contribution of epigenetics in this process remains unknown. Here using avian epidermis we find two major strategies regulate β-keratin gene clusters. 1) Over the body, macro-regional specificities (scales, feathers, claws, etc) established by typical enhancers control five sub-clusters located within the epidermal differentiation complex on chromosome 25; 2) Within a feather, micro-regional specificities are orchestrated by temporo-spatial chromatin looping of the feather β-keratin gene cluster on chromosome 27. Analyses suggest a 3-factor model for regional specification: competence factors (e.g., AP1) make chromatin accessible, regional specifiers (e.g., Zic1) target specific genome regions, and chromatin organizers (e.g., CTCF, SATB2) establish looping configurations. Gene perturbations disrupt morphogenesis and histo-differentiation. This chicken skin paradigm advances our understanding of how regulation of big gene clusters can set up a two-dimensional body surface map.

overall_design: To understand the transcriptional and epigenetic control of Keratin gene clusters during embryonic skin specification, we examined region-specific expression patterns and quantified both gene expression and histone modifications of major Keratin clusters at three stages of skin development. We used embryonic day 7 (E7) dorsal back epidermis, which shows no region-specific development, E9 dorsal back and leg epidermis, which shows the beginning of feather specification on the back but no specification on legs yet, as well as E14 dorsal back and leg epidermis, which shows completely specified feather and scale epidermis, respectively. To test the hypothesis that intra-cluster chromatin looping controls differential Feather Keratin (FK) gene expression of the Chr27 β-keratin cluster, we examined whether higher-order chromatin interactions occur within the cluster in chick embryonic skin epidermis using Next-Generation Capture-C. We used dorsal skin epidermis (experimental group) and whole brain (control group) collected at different developmental stages (E7 and E14). We selected six sites, Pk1, Pk12, Pk18, Pk28, and FK42, randomly across the whole Chr27 β-keratin gene cluster to design Capture-C probes/baits. We generated two duplicate Capture-C libraries for each tissue. Since skin is afforded additional functions by the presence of diverse skin appendages in different regions, we classified “regional differences” into macro and micro differences, indicating differences across different body parts (feather versus scale) and within an appendage (dorsal and wing feather barb branch), respectively.

first: Jie

last: Yan

first: Ping

last: Wu

first: Ting-Xin

last: Jiang


title: RIPK1 gene variants associate with increased obesity in humans and can be therapeutically silenced to improve metabolic dysfunction in obese mice

status: Public on Jun 06 2020

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

type: Expression profiling by high throughput sequencing

summary: Obesity is a major public health burden worldwide, greatly increasing the risk of diabetes, cardiovascular diseases and cancer. Obesity and associated insulin resistance are characterized by chronic low-grade inflammation driven by the cooperation of the innate immune system and dysregulated metabolism in adipose tissue and other metabolic organs. RIPK1 (Receptor-Interacting serine/threonine Protein Kinase 1) is a central regulator of inflammatory cell function that coordinates inflammation, apoptosis and necroptosis in response to inflammatory stimuli. Here, we show that genetic polymorphisms near the human RIPK1 locus associate with increased RIPK1 gene expression in adipose tissue and are strongly linked with the risk of obesity in a human population. We show that one of these SNPs is within a binding site for E4BP4 and increases RIPK1 promoter activity and RIPK1 gene expression in adipose tissue.  Therapeutic silencing of RIPK1 in vivo in a mouse model of diet-induced obesity dramatically reduces fat mass, total body weight and improves insulin sensitivity, while simultaneously reducing macrophage and promoting invariant natural killer T-cell accumulation in adipose tissue. These findings demonstrate RIPK1 is a genetic driver of obesity in humans, and that reducing RIPK1 expression is a potential novel therapeutic approach to target obesity and related diseases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA sequencing (scRNA-seq) profiles of adipose tissues from mice treated with Control or RIPK1-targeting antisense oligonucleotides, and scRNA-seq profiles of human omentum.

middle: P

first: Katey

last: Rayner


title: Genome-wide methylation changes in maternal microchimeric cells from Mmc+ and Mmclow offspring mice

status: Public on Jun 04 2020

city: Hamburg

first: Jiabin

last: Huang

address: Martinistr. 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

type: Methylation profiling by high throughput sequencing

summary: During mammalian pregnancy, immune cells are vertically transferred from mother to fetus. The functional role of these maternal microchimeric cells (MMc) is largely unknown. We show that MMc induce a preferential differentiation of hematopoietic stem and progenitor cells towards myelopoiesis in bone marrow of fetal mice, and improves resilience against cytomegalovirus infection in neonates. In humans, low MMc counts in cord blood are associated with an increased number of infections in the first year of life primarily in male newborns. Taken together, MMc boost neonatal immunity in mice and humans to mitigate the risk for early life infections.

overall_design: Examination of 2 different methylation changes in maternal microchimeric cells.

first: Denise

last: Ohnezeit

first: Nicole

last: Fischer

first: Ina

middle: A

last: Stelzer

first: Christopher

last: Urbschat

first: Petra

middle: C

last: Arck


title: Expression changes after Inhibition of AHD in Molm-13 cells

status: Public on Jun 03 2020

city: Houston

first: Fangrui

state: Texas

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

summary: Formation of AF9/ENL/AF4/AFF4-containing super elongation complexes (SEC) and catalytic activity of DOT1L are required for MLL-rearranged leukemia. We evaluated gene expression changes after inhibition of AHD in leukemia cells.

overall_design: Molm-13 cells containing MLL-AF9 gene were treated by AHD inhibitor for 4 days, and gene expression changes were monitored.

first: Yongcheng

last: Song

first: Qianxing

last: Mo


title: Screening of PCRP transcription factor antibodies in biochemical assays

status: Public on Jun 09 2020

city: Ithaca

first: B. Franklin

last: Pugh

state: New York

address: 465 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Antibodies offer a powerful means to interrogate specific proteins in a complex milieu, and where epitope tagging is impractical. However, antibody reliability is problematic. The Protein Capture Reagents Program (PCRP) has generated over a thousand renewable monoclonal antibodies against presumptive chromatin proteins in an effort to improve reliability. However, these reagents have not been widely field tested.  We therefore screened them in a variety of chromatin-based assays. 887 unique antibodies against 681 unique chromatin targets were assayed by ChIP-exo. A subset was further tested in ChIP-seq, CUT&RUN, STORM super-resolution microscopy, immunoblots, and PBM protein-DNA interaction assays. At least 5% of the tested antibodies were clearly validated by the most stringent of criteria. However, many others produced data that was distinctly different from background, but whose validity was ambiguous. We demonstrate and discuss the metrics and limitation to antibody validation in chromatin-based assays.

overall_design: Large scale screen of PCRP antibodies with ChIP-exo

first: William

middle: K

last: Lai

first: Prashant

last: Kuntala

first: Thomas

middle: R

last: Blanda

first: Kylie

last: Bocklund

first: Josh

last: Mairose

first: Sarah

last: Dweikat

first: Kate

last: Mistretta

first: B

middle: F


title: Putative Regulators for the Continuum of Erythroid Differentiation Revealed by Single-cell Transcriptome of Human BM and UCB Cells[scRNA-seq]

status: Public on May 25 2020

city: Guangzhou

first: Xiangmin

last: Xu

state: Guangdong

address: 1838 Guangzhou Avenue North

department: Department of Medical Genetics

country: China

institute: School of Basic Medical Sciences

summary: Fine-resolution differentiation trajectories of adult human hematopoietic stem cells (HSC) involved in the generation of red cells is critical for understanding dynamic developmental changes that accompany human erythropoiesis. Using Single-cell RNA sequencing (scRNA-seq) of primary human terminal erythroid cells (CD34−CD235a+) isolated directly from adult bone marrow (BM) and umbilical cord blood (UCB), we documented the transcriptome of terminally differentiated human erythroblasts at unprecedented resolution. The insights enabled us to distinguish polychromatic erythroblasts (PolyE) at the early and late stages of development as well as the different development stages of orthochromatic erythroblasts (OrthoE). We further identified a set of putative regulators of terminal erythroid differentiation and functionally validated three of the identified genes, AKAP8L, TERF2IP and RNF10, by monitoring cell differentiation and apoptosis. We documented that knockdown of AKAP8L suppressed the commitment of HSC to erythroid lineage and cell proliferation, and delayed differentiation of colony forming unit-erythroid (CFU-E) to the proerythroblast stage (ProE). In contrast, the knockdown of TERF2IP and RNF10 delayed differentiation of PolyE to OrthoE stage. Taken together, the convergence and divergence of the transcriptional continuums at single-cell resolution underscore the transcriptional regulatory networks that underlie human fetal and adult terminal erythroid differentiation.

overall_design:
CD235a+ cells were isolated from 3 adult bone marrow and 3 umbilical cord blood samples and further sequenced by 10x Genomics platform to obtain transcriptomic profiles.UMI Count matrices were generated by cellranger.

>>> Submitter states that raw data have been deposited in EGA (EGAS00001003114)<<<

first: Peng

first: Yongzhong

last: Zhao

first: Jianmei

last: Zhong


title: CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

summary: Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-seq to monitor the direct effects of rapid CDK12 inhibition on transcription activity and CTD phosphorylation in human cells. CDK12 inhibition causes a genome-wide defect in transcription elongation and a global reduction of CTD Ser2 and Ser5 phosphorylation. The elongation defect is explained by the loss of the elongation factors LEO1 and CDC73, part of PAF1 complex, and SPT6 from the newly-elongating pol II. Our results indicate that CDK12 is a general activator of pol II transcription elongation and indicate that it targets both Ser2 and Ser5 residues of the pol II CTD.

overall_design: After CDK12 inhibition for 15 minutes with 1-NM-PP1 in HEK293 CDK12as cells, we performed mNET-seq (total pol II, Ser2P (with two different antibodies), and Ser5P) and ChIP-seq for total pol II, Ser2P, Ser5P, LEO1, SPT6, and CPSF73. In wild-type HEK293 cells, we performed ChIP-seq for total pol II after treatment with DMSO or 1-NM-PP1 for 15 minutes.

first: Justyna

last: Zaborowska

first: Livia

last: Caizzi

first: Eusra

last: Mohammad

first: Taras

last: Velychko

first: Björn

last: Schwalb

first: Ivan

last: Ferrer-Vicens

first: Daniel

last: Blears

first: Takayuki

last: Nojima

first: Patrick

last: Cramer

first: Shona

last: Murphy


title: Disome and trisome profiling reveal targets of ribosome quality control

status: Public on May 26 2020

city: Bethesda

first: Nicholas

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

summary: The ribosome-associated protein quality control (RQC) system that resolves stalled translation events is activated when ribosomes collide and form disome, trisome or higher order complexes. However, it is unclear whether this system distinguishes collision complexes formed on defective mRNAs from those with functional roles on endogenous transcripts. Here, we performed disome and trisome footprint profiling in yeast and found collisions were enriched on diverse sequence motifs known to slow translation. When 60S recycling was inhibited, disomes accumulated at stop codons and could move into the 3’UTR to reinitiate translation. The ubiquitin ligase and RQC factor Hel2/ZNF598 generally recognized collisions but did not trigger degradation of endogenous transcripts. However, loss of Hel2 triggered the integrated stress response, via phosphorylation of eIF2alpha, thus linking these pathways. Our results suggest that Hel2 has a role in sensing ribosome collisions on endogenous mRNAs and such events may be important for cellular homeostasis.

overall_design: 31 samples are included in the study (4 mRNA-Seq, 4 monosome footprints, 21 disome footprints, and 2 trisome footprints). Read sizes were examined according to lengths relevant for each type of analysis and aligned by 5' or 3' ends, as noted. Samples also differ according to media conditions (3-AT, anisomycin, etc.) and genotype. Some samples serve as biological replicates, as noted.

first: Sezen

last: Meydan


title: poly(UG)-tailed RNAs in Genome Protection and Epigenetic Inheritance [ncRNA-Seq]

status: Public on May 12 2020

city: Boston

first: Aditi

last: Shukla

state: MA

address: 77 Avenue Louis Pasteur, NRB 266

department: Genetics

institute: Harvard Medical School

summary: Mobile genetic elements threaten genome integrity in all organisms. MUT-2/RDE-3 is a ribonucleotidyltransferase required for transposon silencing and RNA interference (RNAi) in C. elegans. When tethered to RNAs in heterologous expression systems, RDE-3 can add long stretches of alternating non-templated uridine (U) and guanosine (G) ribonucleotides to the 3’ termini of these RNAs (polyUG or pUG tails). Here, we show that, in its natural context in C. elegans, RDE-3 adds pUG tails to transposon RNAs, as well as to targets of RNAi. pUG tails with more than 16 perfectly alternating 3’ U and G nucleotides convert RNA fragments into agents of gene silencing. pUG tails promote gene silencing by recruiting RNA-dependent RNA Polymerases (RdRPs), which use pUG-tailed RNAs (pUG RNAs) as templates to synthesize small interfering RNAs (siRNAs). Our results show that cycles of pUG RNA-templated siRNA synthesis and siRNA-directed mRNA pUGylation underlie dsRNA-directed transgenerational epigenetic inheritance in the C. elegans germline. We speculate that this pUG RNA/siRNA silencing loop allows parents to inoculate progeny against the expression of unwanted or parasitic genetic elements.

overall_design: Small RNA-seq on 2 biological replicates of rde-1(ne219); oma-1(zu405) animals injected with either an oma-1 pGC RNA or an oma-1 pUG RNA. Noninjected animals serve as negative controls.

first: Jenny

last: Yan

first: Yuhan

last: Fei

first: Scott

last: Kennedy


title: poly(UG)-tailed RNAs in Genome Protection and Epigenetic Inheritance [RNA-Seq]

overall_design: mRNA-seq on 2 biological replicates of WT (N2) vs. rde-3 (YY1449) adult animals.

middle: J

last: Pagano

first: Josh

last: Gorham

first: J

middle: G

last: Seidman


title: poly(UG)-tailed RNAs in Genome Protection and Epigenetic Inheritance

type: Non-coding RNA profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Anaerobic sulfur oxidation underlies adaptation of a chemosynthetic symbiont to oxic-anoxic interfaces

status: Public on Apr 30 2020

city: Vienna

first: Lena

last: König

address: Althanstrasse 14

country: Austria

institute: University of Vienna

summary: Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by monocultures of thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. Here, by applying omics, Raman microspectroscopy and stable isotope labeling, we investigated the effect of oxygen on the metabolism of Candidatus Thiosymbion oneisti. Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation, organic carbon assimilation and polyhydroxyalkanoate (PHA) biosynthesis, as well as nitrogen fixation and urea utilization were upregulated in oxic conditions. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand its deleterious effects, and fewer symbionts were detected to divide. Based on this first global physiological study of an uncultured chemosynthetic ectosymbiont, we propose that, in anoxic sediment, its proliferation is powered by anaerobic sulfur oxidation coupled to denitrification, whereas in upper layers it makes use of aerobic respiration to facilitate assimilation of carbon and nitrogen, and to survive oxidative stress. The ectosymbiont’s versatile metabolism is thus well-adapted to exploiting a highly changeable environment.

overall_design: rRNA-depleted total RNA was sequenced (RNA-Seq) of symbiotic nematodes (50 per sample) that were incubated for 24 h under 4 different conditions (oxic, hypoxic, anoxic, anoxic-sulfidic)

first: Gabriela

last: Paredes

first: Tobias

last: Viehboeck

first: Raymond

last: Lee

first: Marton

last: Palatinszky

first: Michaela

last: Mausz

first: Sigfried

last: Reipert

first: Arno

last: Schintlmeister

first: Andreas

last: Maier

first: Jean-Marie

last: Volland

first: Claudia

last: Hirschfeld

first: Michael

last: Wagner

first: David

last: Berry

first: Stephanie

last: Markert

first: Silvia

last: Bulgheresi


title: Transcriptomic analysis of stress response to novel antimicrobial coatings in a clinical MRSA strain

status: Public on Apr 22 2020

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: Effect of two different antimicrobial materials, functionalized graphene oxide (GOX), and AGXX® coated on cellulose fibers, on the growth and transcriptome of the clinical MRSA strain S. aureus 04-02981. In addition, we investigated the effect of a third material as a combination of GOX and AGXX® fibers on S. aureus 04-02981

overall_design: 26 samples;  5 samples and 5 time points; no replicates

first: A

last: Vaishampayan

first: R

last: Ahmed

first: O

last: de Jong

last: Haag

last: Kok

first: E

last: Grohmann


title: poly(UG)-tailed RNAs in Genome Protection and Epigenetic Inheritance [other]

first: Aditi

last: Shukla

overall_design: oma-1 pUG RNAs were sequenced in WT (N2) vs. rde-3(ne3370) mutant (YY1449) adult animals using an Illumina MiSeq. Animals were fed either an empty vector control (L4440) or dsRNA targeting the gene oma-1 (Ahringer library clone or custom clone pAS74, which targets exon 6 of oma-1). oma-1 pUG RNAs from F1-F4 descendants of pAS74-fed animals were also sequenced.

middle: E

last: Dodson

first: Scott

last: Kennedy


title: SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues

status: Public on Apr 23 2020

city: Cambridge

first: Alex

last: Shalek

address: 45 Carleton Street

department: Chemistry

institute: MIT

summary: There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) which causes the disease COVID-19. SARS-CoV-2 spike (S)-protein binds ACE2, and in concert with host proteases, principally TMPRSS2, promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues, and the factors that regulate ACE2 expression, remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 amongst tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung type II pneumocytes, ileal absorptive enterocytes, and nasal goblet secretory cells. Strikingly, we discover that ACE2 is a human interferon-stimulated gene (ISG) in vitro using airway epithelial cells, and extend our findings to in vivo viral infections. Our data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection.

sample_organism:
Macaca fascicularis
Macaca mulatta
Homo sapiens
Mus musculus

overall_design:
Samples from 8 datasets are included: single-cell RNA-Seq studies: 2 human adult donors of inferior turbinate scrapings with two replicates each. Four mouse donors of nasal epithelial cells, two stimulated with IFNA and two controls with two replicates from each animal. 5 non-human primate SHIV and healthy lung donors. 3 non-human primate SHIV and healthy Ileum donors.  13 human ileal small intestine donors. 10 mTB-infected non-human primates with 4 samples of granulomas from each and one sample of uninvolved lung lobe from each. 8 human lung tissue donors with mTB infection, mTB infection and HIV, or no mTB infection. Bulk RNA-seq samples: Two human donors stimulated with three replicates of each stimulation with IFNA, IFNG, IL17A, or IL4, each at increasing doses (0, 0.1 ,0.5, 1, 2, 5, 10 ng/mL) and 12 replicates of unstimulated samples. One mouse donor of cells from the trachea with three replicates of each stimulation with IFNA, IFNB, or IFNG, each at increasing doses (0, 0.1 ,0.5, 1, 2, 5, 10 ng/mL) and 12 replicates of unstimulated samples. One human cell line stimulated with three replicates of each stimulation with IFNA, IFNG, IL17A, or IL4, each at increasing doses (0, 0.1 ,0.5, 1, 2, 5, 10 ng/mL) and 12 replicates of unstimulated samples.
Submitter declares that the human raw data will be deposited in dbGaP due to patient privacy concerns.'

first: Carly

last: Ziegler

first: Samuel

last: Allon

first: Sarah

last: Nyquist

first: Ian

middle: M

last: Mbano

first: Vincent

middle: N

last: Miao

first: Constantine

last: Tzouanas

first: Yuming

last: Cao

first: Ashraf

middle: S

last: Yousif

first: Julia

last: Bals

first: Blake

last: Hauser

first: Jared

last: Feldman

first: Christoph

last: Muus

first: Marc

middle: H

last: Wadsworth II

middle: W

last: Kazer

first: Travis

last: Hughes

first: Benjamin

last: Doran

first: G

last: Gatter

first: Marko

last: Vukovic

first: Faith

last: Taliaferro

first: Ben

last: Mead

first: Zhiru

last: Guo

first: Jennifer

last: Sucre

first: Chase

last: Taylor

first: Brian

last: Lin

first: Avinash

last: Waghray

first: Vanessa

last: Mitsialis

first: Daniel

last: Dwyer

first: Kathleen

last: Buchheit

first: Joshua

last: Boyce

first: Nora

last: Barrett

first: Tanya

last: Laidlaw

first: Shaina

middle: L

last: Carroll

first: Lucrezia

last: Colonna

first: Victor

last: Tkachev

first: Christopher


title: Expression data from water extracted olive leaf (WOL)-treated CD34+ cells

status: Public on Apr 17 2020

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

summary: Gene expression profiling reveals a potential role of WOL in differentiation of CD34+ cells towards erythropoiesis

overall_design:
Microarray gene expression profiling was conducted for three replicates of OLE-treated CD34+ cells on day 12 and untreated control cells on day 0 and day 12.
RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual (P/N 08-0306). Human genome array strips (HG-U219) were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: MYC functions as a switch for natural killer cell-mediated immune surveillance of lymphoid malignancies

status: Public on Apr 20 2020

city: Monrovia

first: Srividya

last: Swaminathan

state: CA

address: 1218 S. Fifth Ave

department: Systems Biology

institute: City of Hope

summary: We delineate the immunobiology during MYC oncogene-driven lymphomagenesis by RNA sequencing analysis followed by CIBERSORT of bulk splenic samples from healthy and SRa-tTA/tet-O-MYC mice before and after MYC inactivation. The data set also delineates global changes in signaling molecules in healthy spleens (controls) and lymphomagenic spleens in MYC ON and MYC OFF states.

overall_design: mRNA profiles of splenic single cell suspensions from healthy normal (FVB/N), SRa-tTA/tet-O-MYC (MYC ON), and SRa-tTA/tet-O-MYC (MYC OFF/ Doxycycline) mice, in triplicate were analyzed using Beijing Genomics Institute (BGI) Sequencing (BGISEQ-500).

first: Renumathy

last: Dhanasekaran

first: Dean

last: Felsher


title: Transforming Growth Factor-b Suppresses Type 2 Immunity to Cancer

status: Public on May 29 2020

city: New York

first: Fengshen

last: Kuo

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: The immune system employs two distinct defense strategies against infections: pathogen elimination typified by type 1 immunity, and pathogen containment exemplified by type 2 immunity concomitant with tissue repair.  Akin to infectious diseases, cancer progresses with cancer cell acquisition of microorganism-like behavior propagating at the expense of the host.  While immunological mechanisms of cancer cell elimination are well defined, whether immune-mediated cancer cell containment can be induced is poorly understood.  Here we show that ablation of transforming growth factor-β receptor II (TGFβRII) in CD4+ T cells promotes tumor tissue healing and halts cancer progression.  The restorative response is associated with remodeling of the blood vasculature patterning with cancer cell hypoxia and death instigated in avascular regions, a process dependent on the T helper 2 cytokine IL-4.  Thus, type 2 immunity represents an effective cancer defense mechanism, and TGFβ signaling in helper T cells may be targeted for tissue-level cancer immunotherapy.

overall_design: Tumor-infiltrating CD4+CD25- T cells were collected from 23-week-old Tgfbr2fl/flPyMT (wild-type, WT; n=2 replicates), ThPOKCreTgfbr2fl/flPyMT (knockout, KO; n=2 replicates with 2 technical repeats, i.e., independent library prepared from the same RNA extraction), Il4-/-Tgfbr2fl/flPyMT (Il4-/-; n=2 replicates) and Il4-/-ThPOKCreTgfbr2fl/flPyMT (Il4-/-KO; n=2 replicates) mice.

first: Ming

last: Liu

last: Li


title: Comparative analysis of genome-wide UV repair events in two primates show different rates but similar distribution.

status: Public on Apr 06 2020

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mahalle, Üniversite Caddesi No:27 Tuzla, Sabancı Üniversitesi

department: Mol. Bio. Genetics & Bioeng.

country: Turkey

institute: Sabanci University

summary: Nucleotide excision repair is a primary DNA repair mechanism that removes bulky DNA adducts such as UV-induced pyrimidine dimers. Correspondingly, genome-wide mapping of nucleotide excision repair with eXcision Repair sequencing (XR-seq), provides comprehensive profiling of DNA damage repair. A number of XR-seq experiments at a variety of conditions for different damage types revealed heterogenous repair in the human genome. Although human repair profiles were extensively studied, how repair maps vary between primates is yet to be investigated. Here, we characterized the genome-wide UV-induced damage repair maps of the grey mouse lemur,Microcebus murinus, in comparison with human. We derived fibroblast cell lines from mouse lemur and exposed them to UV irradiation. Following repair events were captured genome-wide by XR-seq protocol 1 hour and 5 minutes after irradiation for cyclobutane pyrimidine dimers (CPD) and 6-4 pyrimidine-pyrimidone photoproducts ([6-4]PP), respectively. Mouse lemur repair profiles were analyzed in comparison with the equivalent human fibroblast datasets. We found that transcription-coupled repair levels for CPD repair differs between two primates. Despite this, comparative analysis of human and mouse lemur fibroblasts revealed that genome-wide repair profiles of the homologous regions between the primates are highly correlated. This correlation is stronger for the highly expressed genes as well as the genes sharing high homology. With the inclusion of an additional XR-seq sample derived from another human cell line in the analysis, we found that fibroblasts between two primates repair lesions more similarly relative to two distinct cell lines from human. These results suggest that mouse lemurs and humans, and possibly primates in general, share similar repair mechanism as well as genomic variance distribution.

sample_organism:
Homo sapiens
Microcebus murinus

platform_organism:
Homo sapiens
Microcebus murinus

overall_design: Examination of genome-wide UV repair events in mouse lemur and human fibroblasts

first: Ümit

last: Akköse

first: Veysel

middle: O

last: Kaya

first: Laura

last: Lindsey-Boltz

first: Zeynep

last: Karagöz

first: Adam

middle: D

last: Brown

first: Beth

last: Sullivian

first: Peter

last: Larsen

first: Anne

last: Yoder

first: Aziz

last: Sancar

first: Ogün


title: Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates

city: University Park

first: Nabeel

last: Ahmed

state: PENNSYLVANIA

address: 407 Chemistry Building

department: The Huck Institutes of the Life Sciences

institute: Pennsylvania State University

summary: Variation in translation-elongation kinetics along a transcript’s coding sequence plays an important role in the maintenance of cellular protein homeostasis by regulating co-translational protein folding, localization, and maturation. Translation-elongation speed is influenced by molecular factors within mRNA and protein sequences. For example, when proline is present in the ribosome’s P- or A-site translation slows down, but the effect of other pairs of amino acids, in the context of all 400 possible pairs, has not been characterized. Here, we study Saccharomyces cerevisiae using a combination of mutational experiments, bioinformatics, and evolutionary analyses, and show that many different pairs of amino acids and their associated tRNA molecules predictably and causally encode translation rate information when these pairs are present in the A- and P-sites of the ribosome independent of other factors known to influence translation speed, including mRNA structure, wobble base pairing, tripeptide motifs, positively charged upstream nascent chain residues, and cognate tRNA concentration. The fast-translating pairs of amino acids that we identify are enriched seven-fold relative to the slow-translating pairs across Saccharomyces cerevisiae’s proteome, while the slow-translating pairs are enriched downstream of domain boundaries. Thus, the chemical identity of amino acid pairs contributes to variability in translation rates, elongation kinetics are causally encoded in the primary structure of proteins, and signatures of evolutionary selection indicate their potential role in co-translational processes.

overall_design: Ribosome profiling of mutant strains with mutations spread across 5 genes in S288C yeast cells

first: Ulrike

last: Friedrich

first: Pietro

last: Sormanni

first: Prajwal

last: Ciryam

first: Bernd

last: Bukau

first: Guenter

last: Kramer

first: Edward

middle: P

last: O'Brien


status: Public on Mar 24 2020

city: Tokyo

first: Takeshi

last: Nitta

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Immunology,

institute: Graduate School of Medicine and Faculty of Medicine, The University of Tokyo

summary: We performed RNA sequencing (RNA-seq) on thymic fibroblasts, thymic epithelial cells, endothelial cells, pericytes, dendritic cells, and lymph node fibroblastic reticular cells.

overall_design: RNA-seq analysis on thymic stromal cells isolated from WT or LTbR-deficient mice.


title: Embryonic Endothelial Evolution towards First Hematopoietic Stem Cells Revealed by Single-Cell Transcriptomic and Functional Analyses

city: Beijing

first: Zongcheng

last: Li

address: No. 8 East Street, Fengtai District

institute: Fifth Medical Center of Chinese PLA General Hospital

summary: Hematopoietic stem cells (HSCs) in adults are believed to be born from hemogenic endothelial cells (HECs) in mid-gestational mouse embryos. Due to rare and transient nature, the HSC-competent ECs have never been stringently identified and accurately captured, let alone their genuine vasculature precursors. Here, we firstly used high-precision single-cell transcriptomics to unbiasedly examine relevant EC populations at continuous developmental stages and transcriptomically identified putative HSC-primed HECs. Combining computational prediction and in vivo functional validation, we precisely captured HSC-competent HECs by newly constructed Neurl3-EGFP reporter mouse model, and realized enrichment further by surface marker combination. Surprisingly, endothelial-hematopoietic bi-potential was rarely but reliably witnessed in culture of single HECs. Noteworthy, primitive vascular ECs experienced two-step fate choices to become HSC-primed HECs, resolving several previously observed contradictions. Taken together, comprehensive understanding of endothelial evolutions and molecular programs underlying HSC-primed HEC specification in vivo will facilitate future investigations directing HSC production in vitro.

overall_design: We initially sequenced 662 single cells from E9.5-E11.0 body and DA of totally 29 embryos. Additionally, we also sequenced 96 single cells with a PK44 immunophenotype (CD41-CD43-CD45-CD31+CD201+Kit+CD44+) from E10.0 AGM regions of totally 9 embryos, 47 T1 pre-HSCs (CD31+CD45-CD41lowKit+CD201high) from E11.0 AGM regions of totally 18 embryos, 48 single cells with an immunophenotype of CD41-CD43-CD45-CD31+CD44+Neurl3-EGFP+ from Neurl3-EGFP reporter mouse embryos and 579 single cells from E8.0-E9.0 body of 24 embryos. In total, 1,432 single cells were sequenced. For each embryo, the embryo proper was isolated and the head, limb buds, heart, visceral bud, and vitelline and umbilical vessels outside the embryo proper were excluded. To specifically capture aortic luminal ECs of AGM region, we performed microinjection of fluorescent dye Oregon green into the dorsal aortas of E10.0-E11.0 embryos as reported. The sampled cells were purified by FACS as CD45-CD31+CD144+, which contained predominantly vascular ECs and CD41+ hematopoietic cells. Meanwhile, CD45-CD31-CD144- non-EC cells in the body were used as negative controls.

first: Siyuan

last: Hou

first: Xiaona

last: Zheng

first: Yun

last: Gao

first: Ji

last: Dong

first: Bing

last: Liu

first: Fuchou

last: Tang

first: Yu

last: Lan


title: Transcriptomic Analysis Links the Response of Diverse Hypothalamic Cell Types to Sustained Diabetes Remission Induced by Fibroblast Growth Factor 1 [single-cell RNA-seq]

status: Public on Apr 21 2020

city: Copenhagen

first: Tune

middle: Hannes

last: Pers

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen

summary: In rodent models of type 2 diabetes (T2D), sustained remission of hyperglycemia can be induced by a single intracerebroventricular (icv) injection of fibroblast growth factor 1 (FGF1), and the hypothalamus was recently identified as a key target for this effect. To investigate how FGF1 action in this brain area achieves this effect, we combined single-nucleeus RNA sequencing (RNA-seq) with single-cell and traditional RNA-seq to identify >70,000 single-cell transcriptomes from the hypothalamus of diabetic Lepob/ob mice obtained on Days 1, 5 and 42 after icv injection of either FGF1 or vehicle. In addition to robust transcriptomics effects on Agrp neurons, which persisted through Day 42, rapid inhibition of Agrp neurons by FGF1 was shown by both electrophysiology and cFos studies. This effect is predicted to increase hypothalamic melanocortin signaling, and we show that FGF1-induced diabetes remission is melanocortin-dependent, as it was prevented by either genetic or pharmacological blockade of central melanocortin receptors. Combined with dramatic transcriptional and morphological changes induced by icv FGF1 injection in tanycytes, astrocytes and oligodendrocytes, including increased cellular contacts between astrocytes and Agrp neurons, these findings implicate glial-neuron interactions as mediators of the sustained remission of diabetes induced by the hypothalamic action of FGF1 action.

overall_design: Single-nucleus and single-cell RNA sequencing (10X genomics Chromium system) and bulk RNA-sequencing

first: Marie

middle: A

last: Bentsen

first: Dylan

last: Rausch

first: Michael

last: Schwartz


title: Fighting against promoter DNA hyper-methylation: Protective histone modification profiles of stress-resistant intestinal stem cells [ChIP-Seq]

status: Public on Mar 07 2020

city: Leipzig

first: Torsten

last: Thalheim

address: Härtelstr. 16 – 18

department: Interdisciplinary Centre for Bioinformatics

institute: Leipzig University

summary: Aberrant DNA methylation in stem cells is a hallmark of aging and tumor development. Recently, we have suggested that promoter DNA hyper-methylation originates in DNA repair and that even successful DNA repair might confer this kind of epigenetic long-term changes. We here ask for interrelations between promoter DNA methylation and histone modification changes observed in the intestine weeks after irradiation and/or following Msh2 loss. We focus on H3K4me3 recruitment to the promoter of H3K27me3 target genes. By RNA- and histone ChIP- sequencing, we demonstrate that this recruitment occurs without changes of the average gene transcription and does not involve H3K9me3. Applying a mathematical model of epigenetic regulation of transcription, we show that the recruitment can be explained by stronger DNA binding of H3K4me3 and H3K27me3 histone methyl-transferases as a consequence of lower DNA methylation. This scenario implicates stable transcription despite of H3K4me3 recruitment, in agreement with our RNA-seq data. Following several kinds of stress, including moderate irradiation, stress-sensitive intestinal stem cell (ISCs) are known to become replaced by more resistant populations. Our simulation results suggest that the stress-resistant ISCs are largely protected against promoter hyper-methylation of H3K27me3 target genes.

overall_design: Examination of histone H3K9 modifications in proximal jejunum tissue from irradiated and non-radiated VC+/?Msh2LoxP/LoxP (Msh2-/-) and VC-/-Msh2loxP/loxP (Msh2+/+) mice in duplicate

first: Lydia

last: Hopp

first: Maria

last: Herberg

first: Susann

last: Siebert

first: Christiane

last: Kerner

first: Marianne

last: Quaas

first: Michal

middle: R

last: Schweiger

first: Joerg

last: Galle

first: Gabriela

last: Aust


title: Fighting against promoter DNA hyper-methylation: Protective histone modification profiles of stress-resistant intestinal stem cells [RNA-Seq]


title: Fighting against promoter DNA hyper-methylation: Protective histone modification profiles of stress-resistant intestinal stem cells


title: Targeting T-cell Lymphoma Epigenome Induces Cell Death, Cancer Testes Antigens, Immune Modulatory Signaling Pathways

status: Public on Apr 04 2020

first: Owen

last: O"Connor

state: NY

address: 51 West 51st Street

department: enter for Lymphoid Malignancies

institute: Columbia University Medical Center

summary: We perform expression analysis on a panel of four T-cell lymphoma lines exposed to romidepsin and 5-azacytidine as single agent and combination.

overall_design: Gene expression profiles of cells exposed and not exposed to romidepsin and 5-azacytidine.

last: O'Connor

first: Luigi

last: Scotto


title: Cytosolic dsRNA-induced gene expression in mouse RAW24.7 macrophages and FIP200 knockout RAW cells

status: Public on Mar 16 2020

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

summary: Our preliminary data showed that FIP200 is essential for dsRNA-induced interferon production. To corroborate the role of FIP200 in RIG-I signaling pathway, we are going to examine the cytosolic dsRNA-induced gene expression in mouse RAW24.7 macrophages and FIP200 knockout RAW cells.

overall_design: RNA sequencning of  mouse RAW24.7 macrophages and FIP200 knockout RAW cells

first: Chaoqun

last: Huang

first: Lin

last: Liu

first: Shitao

last: Li


title: Evolutionary adaptation of Aspergillus niger for increased ferulic acid tolerance

status: Public on Feb 26 2020

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

summary: The aim of this study was to find candidate genes in A. niger involved in the increase tolerance against ferulic acid in A. niger Fa6

overall_design: Transcriptome data on aromatic compounds was used to find candidate genes encoding ferulic acid metabolic enzymes

first: Ronnie

last: Lubbers

first: Adiphol

last: Dilokpimol

first: Mao

last: Peng

first: Jaap

last: Visser

first: Kristiina

last: Hildén


title: Elucidating the regulatory elements for transcription termination and post-transcriptional processing in the Streptomyces clavuligerus genome

status: Public on Mar 05 2020

city: Daejeon

first: Soonkyu

last: Hwang

address: 291 Daehakro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

summary: We obtained genome-scale transcript 3' end termini information by term-seq in S. clavuligerus ATCC 27064, and transcription unit were determined by integration of other multi-omics data to elucidate the regulatory elements for transcription termination and post-transcriptional processing.

overall_design: transcript 3' end termini information (term-seq, pooling) of Streptomyces clavuligerus ATCC 27064 at four different growth phases in duplicates using Illumina HiSeq

first: Namil

last: Lee

first: Donghui

last: Choe

first: Yongjae

first: Woori

last: Kim

first: Suhyung

last: Cho

first: Bernhard

last: Palsson

first: Byung-Kwan


title: Genome-wide targets identification by CRISPRi-Omics for high-titer production of free fatty acids in Escherichia coli

status: Public on Mar 03 2020

city: Tianjin

first: Lixia

last: Fang

address: 135 Yaguan Road, Jinnan District

institute: Tianjin University

summary: We employ omics analyses to identify potential targets in multiple cellular processes, enabling systematical discovery of beneficial chromosomal gene targets that can be engineered to optimize free fatty acids (FFAs) production in Escherichia coli. As a result, we identify 56 beneficial genes , including 46 novel targets functioning in cell structure and division, and signaling transduction that efficiently facilitate FFAs production.

overall_design: Transcriptome analyses of three engineered strains LihfA, HfadR and OfadR and the strain Control

first: Yingxiu

last: Cao

first: Hao

last: Song


title: Differential expression among Liver, Bone marrow or Adipose-derived Mesenchymal Stromal Cells

status: Public on Feb 22 2020

city: Rochester

first: Walter

last: Park

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

summary: RNA-seq was performed among 6 liver, 3 bone marrow and 3 adipose derived MSCs.  The results show Liver-MSC is different from BoneMarrow and Adipose derived MSCs.

overall_design: For this comparison 6 liver-MSC specimens were compared to 6 non-liver (3 Bone marrow and 3 adipose) MSC specimens, all derive from diferent humans.

first: Timucin

last: Taner


title: A novel systems biology approach to evaluate mouse models of  late-onset Alzheimer’s disease

status: Public on Feb 03 2020

city: Bar Harbor

first: Christoph

last: Preuss

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary:
Background: Late-onset Alzheimer’s disease (LOAD) is the most common form of dementia worldwide. To date, animal models of Alzheimer’s have focused on rare familial mutations, due to a lack of frank neuropathology from models based on common disease genes. Recent multi-cohort studies of postmortem human brain transcriptomes have identified a set of 30 gene co-expression modules associated with LOAD, providing a molecular catalog of relevant endophenotypes.
Results: This resource enables precise gene-based alignment between new animal models and human molecular signatures of disease. Here, we describe a new resource to efficiently screen mouse models for LOAD relevance. A new NanoString nCounter® Mouse AD panel was designed to correlate key human disease processes and pathways with mRNA from mouse brains. Analysis of three mouse models based on LOAD genetics, carrying APOE4 and TREM2*R47H alleles and the 5xFAD mouse, a widely used amyloid pathology model, demonstrated overlaps with distinct human AD modules that, in turn, are functionally enriched in key disease-associated pathways. Comprehensive comparison with full transcriptome data from same-sample RNA-Seq shows strong correlation between gene expression changes independent of experimental platform.
Conclusions: Taken together, we show that the nCounter Mouse AD panel offers a rapid, cost-effective and highly reproducible approach to assess disease relevance of potential LOAD mouse models

overall_design: In this study, a cohort of 155 mice from four four different strains carrying Alzheimer associated genetic risk variants was used to to correlate key human disease processes and pathways with mRNA from mouse brains. Three novel mouse models, harboring two LOAD risk alleles, were used to translate co-expression profiles between human and mouse brain transcriptome data using our novel Mouse AD panel. Transcriptome analysis was performed for the APOE4 KI mouse, carrying a humanized version of the strongest LOAD associated risk allele (APOE-ε4) and the Trem2*R47H mouse, which harbors a rare deleterious variant in TREM2. The rare TREM2 R47H missense variant (rs75932628) has been previously associated with LOAD in multiple independent studies. In addition, we added the 5xFAD model, a commonly used mouse model carrying transgenes with a total of five AD-linked familial mutations in APP and PSEN1 to our analysis in order to compare our novel LOAD models to a model that resembles the early onset form of the disease with a high amyloid burden.Mouse transcriptome data for half brains was analyzed at different ages (2-14 months) to estimate the overlap with human post-mortem co-expression modules during aging.

first: Gregory

last: Carter


title: Nascent transcriptomics reveal cellular pro-lytic factors upregulated upstream of the latency-to-lytic switch protein of Epstein-Barr virus

status: Public on Jan 13 2020

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Lytic activation from latency is a key transition point in the life cycle of herpesviruses. Epstein-Barr virus (EBV) is a human herpesvirus that can cause lymphomas, epithelial cancers, and other diseases, most of which require the lytic cycle. While the lytic cycle of EBV can be triggered by chemicals and immunologic ligands, the lytic cascade is only activated when expression of the EBV latency-to-lytic switch protein ZEBRA is turned on. ZEBRA then transcriptionally activates other EBV genes and together with some of those gene products ensures completion of the lytic cycle. However, not every latently-infected cell exposed to a lytic trigger turns expression of ZEBRA on, resulting in responsive and refractory subpopulations. What governs this dichotomy? By examining the nascent transcriptome following exposure to a lytic trigger, we find that several cellular genes are transcriptionally upregulated temporally upstream of ZEBRA. These genes regulate lytic susceptibility to variable degrees in latently-infected cells that respond to mechanistically distinct lytic triggers. While increased expression of these cellular genes defines a pro-lytic state, such upregulation also runs counter to the well-known mechanism of viral nuclease-mediated host shut-off that is activated downstream of ZEBRA. Furthermore, a subset of upregulated cellular genes is transcriptionally repressed downstream of ZEBRA, indicating an additional mode of virus-mediated host shut-off through transcriptional repression. Thus, increased transcription of a set of host genes contributes to a pro-lytic state that allows a subpopulation of cells to support the EBV lytic cycle.

overall_design: This study consists of 12 samples.  The EBV-infected cell line HH514-16 was treated with sodium butyrate (NaB) for 3 h, 24 h, and 48 h before RNA labeling with bromouridine.  A paired control (untreated; UT) was prepared for each time point and two experimental replicates were prepared for each of these six conditions.

first: Tiffany

last: Frey

first: Jozan

last: Brathwaite

first: Saurabh

last: Agarwal

first: Mats

last: Ljungman

first: Michael

middle: T

last: McIntosh

first: Sumita

last: Bhaduri-McIntosh


title: Molecular Prognosis of Cardiogenic Shock Patients under Extracorporeal Membrane Oxygenation

status: Public on Dec 31 2019

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
Prognosis for cardiogenic shock patients under ECMO was our study goal. Success defined as survived more than 7 days after ECMO installation and failure died or had multiple organ failure in 7 days. Total 34 cases were enrolled, 17 success and 17 failure.
Peripheral blood mononuclear cells collected at ECMO installation were used analyzed.

overall_design:
Analysis of the cardiogenic shock patients at extracorporeal membrane oxygenation treatment by genome-wide expression and methylation. Transcriptomic profiling and DNA methylation between successful and failure groups were analyzed.
This submission represents the transcriptome data.

first: Tsai-Hsia

last: Hong

first: Hsuan-Yu

last: Chen

first: Sun-Liang


title: Epigenetic silencing of CDR1as drives IGF2BP3-mediated melanoma invasion and metastasis

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptional profile of MESH1-silenced RCC4 cells

status: Public on Jan 26 2020

city: Durham

first: Jen-Tsan

middle: Ashley

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

institute: Duke University

summary: Nutrient deprivation triggers stringent response in bacteria, allowing rapid reallocation of resources from proliferation toward stress survival. Critical to this process is the accumulation of (p)ppGpp regulated by the RelA/SpoT homologues. While mammalian genomes encode MESH1—the homologue of the bacterial (p)ppGpp hydrolase SpoT, neither (p)ppGpp nor its synthetase has been identified in mammalian cells. Therefore, the function of MESH1 remains a mystery. Here, we report that genetic removal of MESH1 from human cell induce an extensive transcriptional response. The changes are distinct from the canonical unfolding protein response but strongly resemble the bacterial stringent response, which induce cell proliferation arrest, implicating MESH1 in a previously uncharacterized stress response in human cells.

overall_design:
human clear cell renal carcinoma cell line RCC4 were transfected by two independent siRNA targeting MESH1 (siMESH1-CDS, siMESH1-3UTR=siMESH1-7002) and compared to the control with non-targeting siRNA (siNT).

siMESH1-CDS: GGGAAUCACUGACAUUGUG, D-031786-01, Dharmacon
siMESH1-3'UTR (siMESH1-7002): CTGAAGGTCTCCTGCTAACTA, SI04167002, Qiagen
non-targeting siRNA (siNT, AllStars Negative Control siRNA, SI03650318).

first: Chien-Kuang

middle: C

last: Ding

first: Kai-Yuan


title: Epigenetic silencing of CDR1as drives IGF2BP3-mediated melanoma invasion and metastasis [RNA-Seq]

summary: Metastasis is the primary cause of death of cancer patients. Dissecting mechanisms governing metastatic spread may uncover important tumor biology and/or yield promising therapeutic insights. Here we investigated the role of circular RNAs (circRNA) in metastasis, using melanoma as a model aggressive tumor. We identified silencing of Cerebellar Degeneration Related 1 (CDR1as), a regulator of the microRNA miR-7, as a hallmark of melanoma progression. We find that CDR1as depletion results from epigenetic silencing of its originating lincRNA, and promotes invasion in vitro and metastasis in vivo, through a miR-7-independent, IGF2BP3-mediated mechanism. Moreover, CDR1as levels identify cellular states associated with distinct therapeutic responses. Our study reveals functional, prognostic and predictive roles for CDR1as and expose circRNAs as key players in metastasis.

overall_design: circRNA profiling analyses were performed on rRNA-depleted RNA-seq of 10 melanoma STCs (single replicates) and 4 cultured melanocytes (single replicates, from ENCODE). rRNA-depleted RNA-seq of additional cultured melanocytes (single replicates of 5 melanocyte cultures from independent donors), melanoma STCs (single replicates of 3 primary-derived STCs), and established melanoma cell lines (2-5 replicates of 7 cell lines) were analyzed for expression of CDR1as and LINC00632. RNA-seq was performed on control and CDR1as-depleted WM278 melanoma cells.

first: Doug

last: Hanniford

first: Eva

last: Hernando


title: Transcriptome Analysis Reveals the Topography of Local Changes after Separate Transformations of the Same Reporter in Hundreds Loci of Yeast

status: Public on Feb 21 2020

city: Guangzhou

first: Qian

last: Gui

address: 74 Zhongshan 2nd Rd

department: Department of Biomedical Informatics

institute: Sun Yat-sen University

summary: "Position effect" means that the activity of an integrated reporter gene (IR) depends on its genomic location. Although the impact of local environment on IR (cis-effect of location) has been widely reported, the impact of IR integration on local environment and its potential mechanism (reaction of location), such as the change of expression landscape and its fitness are poorly understood. Here, we randomly selected ~250 previously constructed strains with GFP gene inserted into hundreds of different locations separately in yeast, and performed high-throughput transcriptome sequencing.

overall_design: We randomly selected ~250 previously constructed strains with GFP gene inserted into hundreds of different locations separately in yeast, and performed high-throughput transcriptome sequencing

first: Shuyun

last: Deng


title: Bronchial epithelial microRNA expression profiling in type 2-low and type 2-high asthma

status: Public on Dec 18 2019

city: Wuhan

first: Guohua

last: Zhen

state: Hubei

address: Jiefang Street No.1095

department: Tongji Medical College, Tongji Hospital

institute: Huazhong University of Science and Technology

summary: Bronchial epithelial brushings were obtained by bronchoscopy from 8 steroid-naïve asthmatics including type 2-low (n=4) and type 2-high asthma (n=4), and 4 healthy controls. The type 2-low and –high asthma was defined by the epithelial expression of a three-gene signature for type 2 status (POSTN, SERPINB2, and CLCA1).

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The differentially expressed miRNAs were identified between: 1) asthmatics versus healthy controls; 2) type 2-high asthma versus type 2-low asthma.

first: Kan

last: Zhang

first: Yuchen

last: Feng

first: Yuxia

last: Liang

first: Wenliang

last: Wu

first: Chenli

last: Chang

first: Dian

first: Shengcong


title: Epigenetic silencing of CDR1as drives IGF2BP3-mediated melanoma invasion and metastasis [RIP-Seq]

overall_design: Three biological replicates of IGF2BP3 RIP-sequencing was performed for WM278 control (shNTC) or CDR1as-depleted (shCDR1as) cells. Input and IGF2BP3 RIP samples were sequenced.


title: Transcriptomics of the plant growth regulator Heatin

status: Public on Dec 01 2019

first: Martijn

last: van Zanten

address: Padualaan 8

department: Institute of Environmental Biology

institute: Utrecht University

summary: Temperature passively affects many biological processes. It is therefore challenging to study dedicated temperature signalling pathways orchestrating plant thermomorphogenesis; a suite of elongation growth-based adaptations that enhance leaf cooling capacity.   Following a chemical genetics approach, we screened a chemical library for compounds that restored abolished hypocotyl elongation in the pif4-2 deficient mutant background in the model plant Arabidopsis thaliana. The small aromatic compound ‘Heatin' (N'-[(2-hydroxy-1-naphthyl)methylene]-2-(1-naphthylamino)propanohydrazide), with 1-aminomethyl-2-naphthol, as minimal active moiety, was isolated as potent enhancer of elongation growth. Here we assessed the transcriptomic changes induced by the compound, by supplementing the MS-agar growth medium with Heatin compared to DMSO solvent, in whole seedlings of the Col-0 wild type background in control (22oC) and high ambient temperature conditions (27oC).

overall_design: Pooled seedlings, grown on sterile MS-agar plates, harvested at dawn of day 3 after initiation of germination (2 day old) and of day 8 (7 day old), in 3 replicates per mutant of 3 pooled independent batches (>50 seedlings per batch), genotype and temperature environment in short day conditions.

first: Lennard

last: van der Woude

first: L

last: Basten Snoek

first: Marcel

last: van Verk


title: Spleen transcriptomes during behavioural fever in Salmo salar

status: Public on Dec 07 2019

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

summary: The transcriptomic analysis was evaluated using RNA-seq of salmon challenged with the birnavirus IPNv under two different thermal conditions: (a) constant temperature (mean temperature 15 ± 0.9 ºC, “No-Fever”) and (b) temperature gradient (mean temperature 15 ± 7.4 ºC, “Fever”). In parallel, fish in another tank were treated by adding 100 ml virus free cell culture supernatant to the water (mean temperature 15 ± 7.4 ºC, "mock-infected"). We identified a specific transcriptomic signature for each group in the RNA-seq data and identifying a set of key components that control inflammatory modulation during behavioural fever upon viral infection in mobile ectotherms.

overall_design: Spleen mRNA profiles were generated by deep sequencing, in triplicate, using Illumina MiSeq. Tisue were obtained from parr Salmo salar at 24, 48, 72- and 96-hours post infection with IPNv and under two different thermal conditions: (a) constant temperature (mean temperature 15 ± 0.9 ºC, “No-Fever”) and (b) temperature gradient (mean temperature 15 ± 7.4 ºC, “Fever”). In parallel, another spleen samples were obtained from salmon exposed at virus-free cell culture supernatant and temperature gradient (mean temperature 15 ± 7.4 ºC, “Mock”).

first: Andrea

last: Aguilar


title: A Phase II Study of Pomalidomide, Daily Low Dose Oral Cyclophosphamide, and Dexamethasone in Relapsed/Refractory Multiple Myeloma

status: Public on Oct 11 2019

city: New York

first: Samir

last: Parekh

address: 1470 Madison Avenue, 5-114, Box 1079

department: Tisch Cancer Institute

institute: Icahn School of Medicine at Mount Sinai

summary: High-througput transcriptome analysis by RNA-seq of multiple myeloma tumor samples (CD138+ cells) in subjects treated with pomalidomide, daily low dose oral cyclophosphamide and dexamethasone in the context of a phase II clinical trial. Samples were collected at baseline as a correlative study to determine whether gene expression profiles could distinguish patients with (un)favorable response to treatment.

overall_design: RNA-seq (NGS) of multiple myeloma tumor samples (CD138+ cells) collected at baseline (T1) in a total of 17 patients.

first: David

last: Melnekoff


title: Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages

status: Public on Nov 27 2019

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

summary: The enteric nervous system (ENS) predominantly originates from vagal neural crest cells (VNC) that emerge from the caudal hindbrain, invade the foregut and populate the gastrointestinal tract. However, the gene regulatory network (GRN) orchestrating the early specification of VNC remains unknown. Using an EdnrB enhancer, we generated a comprehensive temporal map of the chromatin and transcriptional landscape of VNC in the avian model, revealing three VNC cell clusters (neural, neurogenic and mesenchymal), each predetermined epigenetically prior to neural tube delamination. We identify and functionally validate regulatory cores (Sox10/Tfap2B/SoxB/Hbox) mediating each programme and elucidate their combinatorial activities with other spatiotemporally-specific transcription factors (bHLH/NR). Our global deconstruction of the VNC-GRN in vivo sheds light on critical early regulatory mechanisms that may influence the divergent neural phenotypes in enteric neuropathies.

overall_design:
This SuperSeries is composed of the SubSeries listed below.
Refer to individual Series.


title: Effect of disulfiram treatment on pediatric high grade glioma

status: Public on Oct 16 2019

city: London

last: Michod

address: Gower St, Bloomsbury

institute: UCL

summary: RNA-seq analysis was performed to compare gene expression between glioma cells treated with disulfiram and untreated glioma cells.

overall_design: SF188 and GPC16 cells were treated with Disulfiram (SF188: 1 μM, GPC16: 0.32 μM) dissolved in DMSO in presence of 1 μM CuCl2. The same amount of DMSO (without drug) and  CuCl2 was added to the control samples. After 16 h mRNA was isolated and analyzed.

first: Stefanie

last: Meier


title: DNA copy number alteration analysis and gene expression profiles comparing radioresistant to radiosensitive prostate cancer cell lines

city: Dresden

first: Michael

last: Seifert

address: Fetscherstr. 74

institute: TU Dresden

type:
Expression profiling by array
Genome variation profiling by array


title: Effects of Aflibercept administration at 25 mg per kg body weight in retinas of mice subjected to the oxygen-induced retinopathy protocol

status: Public on Oct 01 2019

city: Cambridge

first: Jesus Eduardo

last: Rojo Arias

address: Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary:
We aimed at identifying the regulatory network of Aflibercept in the context of pathological neovascularization by using the oxygen-induced retinopathy mouse model as a surrogate of proliferative diabetic retinopathy
Total RNA was collected from entire retinal cups dissected from mice subjected to the oxygen-induced retinopathy protocol and subsequently injected with Aflibercept either on postnatal day 13 (collection on day 14) or on postnatal day 13 and 15 (collection on day 17). Non-injected OIR littermates and age-matched mice housed in normoxic conditions were used as controls.

overall_design: Three treatments were considered, namely normoxic controls, OIR and OIR+AFL mice. Three mice were considered per treatment, i.e. each group contained three biological replicates. Two ages were considered, namely P14 and P17. Thus, 18 samples were analyzed in total - 2 ages, 3 treatments, and 3 replicates per age and treatment. Each sample consists of total RNA isolated from the 2 entire retinas of 2 mice, i.e. 4 pooled retinas in total.

first: Jesus

first: József

last: Jászai


title: Comparative analysis of gene expression profiles comparing radioresistant to radiosensitive prostate cancer cell lines

summary: Prostate cancer cell lines DU145 and LNCaP were purchased from the American Type Culture Collection. Radioresistant (RR) sublines were generated form these original parental radiosensitive (RS) cell lines. Gene expression profiles of radiosensitive (RS) and radioresistant (RR) prostate cancer cell lines were measured.

overall_design: Three independent experiments were performed for each cell line.

first: Anna

last: Dubrovska

first: Claudia

last: Peitzsch

first: Vasyl

last: Lukiyanchuk


title: Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages [RNA-seq and ChIP-seq]

overall_design:
Transcriptomic and TF binding of avian neural crest cells isolated from their in vivo context at HH12, HH18 and HH25
Authors' note: [1] We electroporated out TF tagged with Avi with a BirA. Then we pulled down with Streptavidin beads. Therefore, no antibodies were used. Plasmids are available on Addgene and deposited appropriately [2] The RNA_featurecount.txt also contains the data from RNA samples in the other subseries (included in the GSE125711 superseries).

first: Irving

last: Ling


title: mRNA expression of colorectal cancer cell line HCT116 transfected with lncRNA-SPRY4-IT1 overexpression or control vector

status: Public on Nov 19 2019

city: shenyang

first: Longyang

last: Jiang

state: liaoning

address: No.77 Puhe Road, Shenyang North New Area, Shenyang,      Liaoning Province, P.R. China

institute: China Medical Univisity

summary: To determine the mRNA expression profile of colorectal cancer cell line HCT116 transfected with lncRNA-SPRY4-IT1 overexpression vector, we performedd gene expression microArray analysis to examine the expression of mRNAs.

overall_design: In this research, there were six samples examed including 3 samples of negtive control cells and 3 samples of SPRY4-IT1 overexpression cells.

first: Lin

last: Zhao


title: Phenotypic plasticity shapes genome architecture in the honeybee Apis mellifera (RNA-seq)

status: Public on Sep 17 2019

city: Dunedin

first: Peter

middle: Kenneth

last: Dearden

address: 710 Cumberland St

department: Department of Biochemistry

country: New Zealand

institute: University of Otago

summary: Female honeybees are specified as workers or queens based on diet during early development.  Workers are essentially sterile with a reduced number of ovarioles and no spermatheca.  In the presence of the queen (queen mandibular pheromone) and her brood, worker ovaries are kept in an inactive quiescent state.  If the queen is removed, or lost, worker bees are able to sense this change in their environment and their ovaries undergo complete remodeling producing unfertilized haploid eggs that will produce male (drone bees).  In this study we analyze gene expression in queen, worker, and laying worker ovaries using RNA-seq and explore differences in the chromatin landscape (focusing on H3K27me3).

overall_design: RNA-seq to measure gene expression in queen, queen right worker and actively laying worker ovaries

first: Elizabeth

middle: J

last: Duncan

first: Megan

last: Leask

middle: K


title: SCDC: Deconvolution of Bulk Gene Expression by Single-Cell RNA Sequencing Data

status: Public on Aug 30 2019

city: Chapel Hill

first: Charles

middle: M.

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: This paper describes SCDC, a deconvolution method for bulk RNA-seq that leverages cell-type specific gene expression profiles from multiple scRNA-seq reference datasets.

overall_design: SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets produced in different conditions, implicitly addressing the batch-effect confounding.

middle: M

first: Aatish

last: Thennavan


title: Phenotypic plasticity shapes genome architecture in the honeybee Apis mellifera (ChIP-seq)

summary: Female honeybees are specified as workers or queens based on diet during early development.  Workers are essentially sterile with a reduced number of ovarioles and no spermatheca.  In the presence of the queen (queen mandibular pheromone) and her brood, worker ovaries are kept in an inactive quiescent state.  If the queen is removed, or lost, worker bees are able to sense this change in their environment and their ovaries undergo complete remodelling producing unfertilised haploid eggs that will produce male (drone bees).  In this study we analyse gene expression in queen, worker, and laying worker ovaries using RNA-seq and explore differences in the chromatin landscape (focussing on H3K27me3).

overall_design: Genome-wide distribution of H3K27me3 was determined by Chromatin immunopreciptation in ovary tissue of queens, sterile workers and workers laying eggs.


status: Public on Sep 13 2019

city: Freiburg

first: Maria Stella

last: Carro

address: Breisacherstraße 64

institute: Freiburg University Medical Center

summary: Genome-wide analysis of GBM-derived brain tumor stem cells-like (BTSCs) collected at the Freiburg Medical Center and UAB (JX6)

overall_design: Total RNA was extracted from BTSCs cultured in Neurobasal supplemented with growth factors (EGF, FGF and LIF)

first: Thomas

last: Unterkircher

first: Maria

middle: S


title: Apoptosis in the fetal testis eliminates developmentally defective germ cell clones

status: Public on Aug 23 2019

city: San Francisco

first: Daniel

last: Nguyen

address: 513 Parnassus Ave

institute: University of California San Francisco

summary: Mammalian egg and sperm are produced by germ cells (GCs) that develop in the embryo long before reproductive maturity. Many GCs that begin this process do not contribute their genes to the next generation, although it remains unclear what determines GC fitness. Here, we examined how the composition of GCs in the fetal testis is affected by scheduled apoptosis as GCs transition between proliferation to sex differentiation. Using multicolored-lineage tracing, we find that apoptosis affects clonally-related GCs, suggesting that this fate decision occurs autonomously based on shared intrinsic properties. Single cell RNA-sequencing reveals extensive heterogeneity among GCs and identifies a Trp53-high subpopulation with elevated apoptotic susceptibility and diminished differentiation. By contrast, the most differentiated subpopulation is depleted for pro-apoptotic transcripts. These results indicate that cell-heritable differences in sex-differentiation segregate GCs into subpopulations with distinct fitness. The reciprocal relationship between sex-differentiation and apoptosis coordinates the removal of developmentally incompetent cells to improve male GC quality.

overall_design: Single cell RNA sequencing of E12.5 and E13.5 male germ cells.

first: D

middle: H

last: Laird


title: Phenotypic plasticity shapes genome architecture in the honeybee Apis mellifera

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Tumors with TSC mutations are sensitive to CDK7 inhibition through NRF2 and glutathione depletion

status: Public on Aug 08 2019

city: Boston

first: Mahsa

last: Zarei

state: Massachusetts

address: 20 Shattuck Street, Thorn Building (D), 823

department: Medicine

institute: BWH

summary: We report the global gene expression effects in TSC-deficient and TSC wild type cells after treatemnet with. CDK7 inhibitor(THZ1), we performed RNA-Seq on TSC1-null HCV.29 cells and TSC1-intact HCV.29 cells treated with 30nM THZ1, and with 100nM THZ1, for 6 hours. Many genes showed marked changes in expression in comparison with control untreated cells.  Furthermore, 1128 genes showed > 5-fold lower expression in 30nM THZ1-treated TSC1-null HCV.29 cells compared with 30nM THZ1-treated TSC1-intact HCV.29 cells.

overall_design: Examination of global gene expression effects in TSC-deficient and TSC wild type cells by RNA-seq  on TSC1-null HCV.29 cells and TSC1-intact HCV.29 cells treated with 30nM THZ1, and with 100nM THZ1, for 6 hours.

first: David

last: Kwiatkowski


title: Validation of  open chromatin interactions predicted from DNA sequences in MCF-7 and K562 cell lines

status: Public on Aug 05 2019

city: Singapore

first: Melissa

middle: Jane

last: Fullwood

address: 14 Medical Drive, #12-01

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is very limited. Here we developed a computational method, Chromatin Interaction Neural Network (CHINN), to predict chromatin interactions between open chromatin regions by using only DNA sequences of the interacting open chromatin regions. CHINN is able to predict CTCF- and RNA polymerase II-associated chromatin interactions between open chromatin regions with good across-sample performances and captures various sequence features that are predictive of chromatin interactions.

overall_design: 4C-seq experiments to validate predicted chromatin interactions at several gene locus.

first: Yan

last: Loh

first: Ying

last: Zhang

first: Fan

last: Cao

first: Yichao

last: Cai


title: Protease-activated receptor-2 promotes osteogenesis in skeletal mesenchymal stem cells at the expense of adipogenesis

status: Public on Aug 16 2019

city: University of Melbourne

last: Pagel

state: Victoria

address: Grattan Street

department: Faculty of Veterinary and Agricultural Sciences

country: Australia

institute: University of Melbourne

summary: Osteoblast-like cells isolated from the calvariae of wildtyope and protease-activated receptor-2 null were treated with unconditioned medium (Control) or medium conditionedby the prostate cancer cell line MDA-PCa-2b (MDA). RNAseq analysis was performed to identify differntially gene expression in wildtype and protease-activated receptor-2 null in response to factors released by prostate cancer cells.

overall_design: Examination of the role of protease activated receptor-2 in the reponse of osteogenic cells to factors released by prostate cancer cells.

first: Eleanor

last: Mackie


title: Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [RNA-seq low input]

status: Public on Jul 26 2019

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

summary: Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how can these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they initiate chromatin remodelling. Here we show that early endoderm binding sites of the paradigm PTF Foxa2 are epigenetically primed by low levels of active chromatin modifications in embryonic stem cells (ESC). Priming of these binding sites is supported by preferential recruitment of Foxa2 to endoderm binding sites compared to lineage-inappropriate binding sites, when ectopically expressed in ESCs. We further show that binding of Foxa2 is required for chromatin opening during endoderm differentiation. However, increased chromatin accessibility was only detected on binding sites which are synergistically bound with other endoderm transcription factors. Thus, our data suggest that binding site selection of PTFs is directed by the chromatin environment and that chromatin opening requires collaboration of PTFs with additional transcription factors.

overall_design: Transcriptional analysis in control and Foxa2-KO ES or endoderm cells; control and Foxa2-overexpressing ES cells.

first: Filippo

first: Gunnar

last: Schotta


title: Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [RNA-seq]

overall_design: Transcriptional analysis in undifferentiated and endo-differentiating DKI mES cells.


title: Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [ChIP-seq Transcription Factors]

overall_design: Transcription factors analysis in  ES, mesendoderm and endoderm cells; control and Foxa2-overexpressing ES cells; Foxa2 and Gata4 overexpressing ES cells.


title: Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [MeDIP-seq]

overall_design: 5mC and 5hmC analysis in undifferentiated and endo-differentiating DKI mES cells.


title: Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [ATAC-seq]

overall_design: Chromatin accessibility  analysis in  ES, mesendoderm and endoderm cells;control and Foxa2 KO ES or endoderm cells; control and Foxa2-overexpressing ES cells; Foxa2 and Gata4 overexpressing ES cells.


title: Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2 [ChIP-seq Histone-Modifications]

overall_design: Histone modifications analysis in  ES, mesendoderm and endoderm cells; Foxa2 over expressing cells ES cells


title: Profiling lncRNAs in the regulatory elements of target genes by chromatin in situ reverse transcription trap sequencing

status: Public on Jun 30 2019

city: Palo Alto

first: Jifan

last: Hu

address: 3801 Miranda Ave, Bldg 100, Room E4-200

department: Palo Alto Veterans Institute for Research

institute: Stanford University Medical School

summary: “chromatin-RNA in situ reverse transcription trap sequencing” (CRIST-Seq) approach was used to profile the RNA interaction network in the promoters of stem cell core factors Sox2 and Oct4

overall_design: Induced pluripotent stem cells (iPSCs) were transfected with CRISPR Cas9 and four gRNAs targeting the Oct4 and Sox2 promoters (Oct4-gRNA and Sox2-gRNA). As the Cas9 control, cells were transfected with CRISPR Cas9 and two random control gRNAs (gCT). Cells were crosslinked with formaldehyde to fix the chromatin structure. RNAs in the chromatin complex of the promoters were in situ reverse transcribed with biotin-dCTP. After immunoprecipitation with Cas9-FLAG antibody, the biotin-cDNAs were separated from genomic DNAs by streptavidin bead purification. The purified biotin cDNAs were used for Illumina library sequencing. An anti-IgG antibody was used as the background control for CRIST immunoprecipitation (IgG-Ct).

first: Shiling

first: Zhonghua

last: Du

first: Yanbao

last: Zhu

first: Jingchen

last: Chen

first: Lin

last: Jia

first: Yichen

last: Wang

first: Cong

first: Andrew

last: Hoffman

first: Jiuwei

last: Cui

first: Ji-Fan


title: Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2


title: Map of dimorphic switching-related signaling pathways in Sporothrix schenckii based on its transcriptome

status: Public on Jun 27 2019

city: Shenyang

first: fangliang

last: zheng

state: Liaoning

address: No. 66 Chongshan Middle Road, Huanggu District

institute: liaoning university

summary: Sporotrichosis, an implantation mycosis caused by the dimorphic fungus Sporothrix schenckii, gained attention over the two last decades due to its broad geographic range and prevalence in tropical and subtropical areas. The dimorphic switching from hyphal form to the yeast form is essential for the pathogenesis of S. schenckii. During the mycelium-to-yeast transition, there are many changes in asexual development, yeast-phase cell formation, cell wall integrity, and melanin synthesis. However, the mechanisms of the signaling pathways associated with these process remain unclear. In this study, transcriptome sequencing of both the yeast stage and mycelium of S. schenckii was carried out. The results showed that 12217 genes, including genes involved in signal transduction and chitin synthesis, were expressed differentially between the two stages. According to these results, a map of the signaling pathways, related to the dimorphic switch, was drawn. Overall, the transcriptome data and analysis presented here lay the foundation for further research into the molecular mechanisms controlling the dimorphic switch of S. schenckii and support the development of anti-S. schenckii strategies targeting genes related to signaling pathways.

overall_design: Examination of transcriptome of hyphal form and yeast form of S. schenckii.

first: Fangliang

last: Zheng

first: Zhenying


title: Transcriptome change after tocilizumab therapy in rheumatoid arthritis patients

status: Public on Jun 06 2019

city: sinjuku-ku

first: Masaru

last: Takeshita

state: Tokyo

address: 35 shinanomachi

department: Division of Rheumatology

institute: Keio University

summary: We compared whole CD4+ and CD8+ T cells from frozen PBMC samples that were collected before and after treatment initiation of each patient with rheumatoid arthritis. Lists consisting of 858 and 950 differentially expressed genes were created from CD4 and CD8, respectively, and these were used for enrichment analysis. As a result, we found that certain pathways were downregulated after TCZ treatment in both CD4+ and CD8+ T cells, including mechanistic target of rapamycin complex 1 (mTORC1) signaling, the IL-2 pathway, and IFN-related genes.

overall_design: Examination between before and after tocilizumab treatment of CD4 and CD8 T cell in rheumatoid arthritis patients

first: Tsutom

last: Takeuchi

first: Yuumi

last: Okuzono


title: High-throughput sequencing identifies 25,303 circRNA targets, including 20,036 known circRNAs and 5,267 uncharacterized circRNAs, in gastric cancer tissues

status: Public on Jun 16 2019

city: Nantong

first: Shan

last: Kong

state: Jiangsu

address: NO.20, Xisi Road

department: Department of Laboratory Medicine

institute: Affiliated Hospital of Nantong University

summary:
Purpose: With the advent of human genome sequencing project, circRNAs attracted widespread attention in cancer research due to its stable ring structure. Our aim was to identify differentially expressed circRNAs in GC and explore their potential roles in GC diagnosis and treatment.
Methods: Total RNA from tissues was isolated by Hipure Total RNA Mini Kit (Magen, Germany). Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, California) was used for RNA concentration measurement while Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA) for RNA integrity estimation. A RIN value over 7.0 was considered eligible. RNA-seq library was prepared with approximately 2μg of total RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina® (Kapa Biosystems, Inc., Woburn, MA). Briefly, total RNA was incubated at 37 °C for 30 min with 10 units RNase R (Epicentre Technologies, Madison, USA) after removing ribosomal RNA. Next, the ribominus RNase R (+) RNAs was fragmented and then first strand and directional second strand synthesis were performed. Then the A tailing and adapter ligation were performed with the purified cDNA. Finally, the purified, adapter-ligated DNA was amplified. Each library was diluted to 10 nM and pooled equimolar prior to clustering. Paired-End (PE150) sequencing was performed on all samples.
Results: A total of 25,303 circRNA targets, including 20,036 known circRNAs and 5,267 uncharacterized circRNAs, were detected and defined. Among them, there were 2,007 circRNAs with statistically significant differences in expression in GC tissues, in which fold changes>2.0 and P<0.05 were identified.

overall_design: Three pairs of gastric cancer tissues and their corresponding adjacent non-cancerous tissues were detected by circRNA-sequencing.

first: Shaoqing

last: Ju

first: Xianjuan

last: Shen


title: High-Spatiotemporal-Resolution Transcriptomes Insights into Fruit Development and Ripening in Citrus sinensis

status: Public on Jun 24 2019

city: Wuhan

first: Juxun

last: Wu

address: No.1 of Shizishan street, Hongshan District

institute: Huazhong Agricultral University

summary: To excavate the underlying molecular regulation network that during citrus fruit development and ripening, we used RNA-seq to generate high-resolution profiles of global gene expression in four different fruit tissues at six development stages. Using weighted gene coexpression network analysis, we identified modules of coexpressed genes and hub genes of tissue-specific networks. In general, this study was aimed to uncover the new molecular insights into citrus fruit development and ripening, and to reveal the specific nonclimacteric characteristics of citrus fruit.

overall_design: Fruit samples of the ‘Fengjie 72-1’ navel orange (C. sinensis L. Osbeck) were harvested at 50, 80, 120, 150, 180 and 220 days after flowring (DAF). Three trees as one biological replicate. Three biological replicates (three trees per replicate) were harvested at each developmental stage. Twelve representative fruits were sampled from each tree at each developmental stage.The four fruit tissues (epicarp, albedo, segment membrane and juice sac) were isolated by hand dissection. A totlal of 72 transcroptomes were sequeced.

first: Guizhi

last: Feng

first: Hualin

last: Yi


title: Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome

status: Public on May 16 2019

city: Daejeon

first: Soonkyu

last: Hwang

address: 291 Daehakro, Yuseong-gu

department: Biological Sciences

institute: KAIST

summary: We obtained the high-quality genome sequence of S. clavuligerus ATCC 27064, and determined genome-wide TSSs. Then, RNA-Seq and ribosome profiling were additionally exploited to reveal fundamental regulatory elements for transcription and translation.

overall_design: Transcriptome (RNA-seq), translatome (ribosome profiling), primary transcriptome (dRNA-seq, pooled) data of Streptomyces clavuligerus ATCC 27064 at four different growth phases in duplicates using Illumina HiSeq

first: Namil

last: Lee

first: Yujin

last: Jeong

first: Yongjae

first: Woori

last: Kim

first: Suhyung

last: Cho

first: Bernhard

middle: O

last: Palsson

first: Byung-Kwan


title: Gene expressions of T cells in each developmental stages in healthy volunteers and patients with rheumatoid arthritis

first: Masaru

summary: We collected and compared samples from the cohort consisted of six groups as follows: methotrexate (MTX) monotherapy, combination therapy of MTX and infliximab (IFX), tocilizumab (TCZ) monotherapy, age- and gender-matched HC, and a small number of synovial fluid samples. In order to reduce variation due to the proportion of cells at each developmental stage, we performed transcriptome analysis after sorting CD4+ and CD8+ T cells according to developmental stage. We created a gene list that was significantly expressed in RA T cells, and revealed that pathways such as mTORC1, IL-2-stat5, Cell cycle and interferon-related genes were significantly enriched among them.

overall_design: Examination among healthy controls and patients with rheumatoid arthritis, including before and after treatment


title: TREM2 Acts Downstream of CD33 in Modulating Microglial Pathology in Alzheimer's Disease

status: Public on Jun 11 2019

city: Charlestown

first: Ana

last: Griciuc

state: MA

address: 114 16th Street

department: Neurology

institute: Massachusetts General Hospital

summary: CD33-/- and/or TREM2-/- mice were crossed with the 5xFAD mouse model of Alzheimer’s disease to generate single and double CD33/TREM2 knock-out mice on 5xFAD background. Transcriptome and gene expression analyses were performed to analyze the impact of CD33 and/or TREM2 knock-out on the transcriptome of microglia in the context of amyloid pathology. The results revealed that CD33 and/or TREM2 knock-out reprogrammed microglial gene expression signatures in 5xFAD mice in an age-dependent manner. Differential gene expression in 5xFAD;CD33-/- microglia depended on the presence of TREM2. These data suggest that TREM2 acts downstream of CD33.

overall_design: Microglia were isolated from brains of WT, 5xFAD, 5xFAD;CD33-/-, 5xFAD;TREM2-/-, and 5xFAD;CD33-/-;TREM2-/- mice at 4 and 8 months of age, using FACS sorting for CD11b and CD45. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen). Libraries were prepared using the TruSeq Stranded mRNA LT Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2500 sequencer using single-end 50. Reads were aligned to mouse genome mm10 using the STAR aligner. Read counts for individual genes were obtained using HTSeq.

first: Shaun

last: Patel

first: Anthony

middle: N

last: Federico

first: Se

last: Choi

first: Brendan

last: Innes

first: Mary

last: Oram

first: Gea

last: Cereghetti

first: Danielle

last: McGinty

last: Anselmo

first: Ruslan

middle: I

last: Sadreyev

first: Suzanne

middle: E

last: Hickman

first: Joseph

last: Khoury

first: Marco

last: Colonna

first: Rudolph

last: Tanzi


title: RETRACTED

status: Public on May 22 2019

city: Orono

first: Benjamin

middle: L

last: King

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

summary: The GSE125987 dataset has been deleted due to retraction of the associated publication.

overall_design: Retracted.


title: Gene expression data of OsHMGB707 overexpression and RNAi transgenic rice plants under normal conditions

status: Public on May 08 2019

city: Shanghai

first: Kai

last: Xu

address: No.2901, Beidi Rd

institute: Shanghai academy of agricultural sciences

summary:
High mobility group (HMG) proteins play an important role in regulation of gene transcription through modulate the structure of DNA. In this study, OsHMGB707, a HMG gene localized in rice drought resistance QTL interval, was isolated and the function on rice stress resistance was identified.  Overexpression of OsHMGB707 significantly enhanced the drought resistance of the transgenic rice plants, whereas the OsHMGB707-RNAi transgenic rice plants exhibited slightly decrease in drought stress tolerance.
To search the downstream genes regulated by OsHMGB707, we performed microarray analysis of the OsHMGB707-overexpressing, OsHMGB707-RNAi and wild-type plants under both normal  conditions using Affymetrix Rice Genome Genechip. 21-day-old plants of the OsHMGB707-overexpressing line OE1, OsHMGB707-RNAi line RNAi1 as well as the wild-type plants were used in the normal condition.

overall_design: The OsHMGB707-overexpression plants,RNAi plants and the wild-type plants were cultured in the culture solution for 21 days.The leaves of the plants were sampled  for RNA isolation, three biological replicate samples each from the OsHMGB707 overexpression, OsHMGB707 RNAi and wild type lines were profiled using rice whole-genome microarrays.

first: Lijun

last: Luo


title: Loss of Msh2 and a single-radiation hit induce common, genome-wide, and persistent epigenetic changes in the intestine

status: Public on Mar 26 2019

city: Leipzig

first: Torsten

last: Thalheim

address: Härtelstr. 16 – 18

department: Interdisciplinary Centre for Bioinformatics

institute: Leipzig University

summary:
Background: Mismatch repair (MMR)-deficiency increases the risk of colorectal tumorigenesis. To determine whether the tumors develop on a normal or disturbed epigenetic background and how radiation affects this, we determined genome-wide histone H3 methylation profiles in macroscopic normal intestinal tissue of young radiated and untreated MMR-deficient VCMsh2LoxP/LoxP (Msh2−/−) mice months before tumor onset.
Results: Histone H3 methylation increases in Msh2−/− compared to control Msh2+/+ mice. Activating H3K4me3 and H3K36me3 histone marks frequently accumulate at genes that are H3K27me3 or H3K4me3 modified in Msh2+/+ mice, respectively. The genes recruiting H3K36me3 enrich in gene sets associated with DNA repair, RNA processing, and ribosome biogenesis that become transcriptionally upregulated in the developing tumors. A similar epigenetic effect is present in Msh2+/+ mice 4 weeks after a single-radiation hit, whereas radiation of Msh2−/− mice left their histone methylation profiles almost unchanged.
Conclusions: MMR deficiency results in genome-wide changes in histone H3 methylation profiles preceding tumor development. Similar changes constitute a persistent epigenetic signature of radiation-induced DNA damage.

overall_design: Examination of 3 different histone modifications in proximal jejunum tissue from irradiated and non-radiated VC+/?Msh2LoxP/LoxP (Msh2-/-) and VC-/-Msh2loxP/loxP (Msh2+/+) mice in duplicate.

first: Maria

last: Herberg

first: Susann

last: Siebert

first: Marianne

last: Quaas

first: Karen

last: Rother

first: Michelle

last: Hussong

first: Janine

last: Altmueller

first: Christiane

last: Kerner

first: Joerg

last: Galle

first: Michal

middle: R

last: Schweiger

first: Gabriela

last: Aust


title: A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes

status: Public on Jan 25 2019

city: Tianjin

first: Bohan

last: Chen

address: NO.94 Weijin Road

institute: Nankai University

summary: Temozolomide (TMZ) is a frequently used chemotherapy for glioma; however, chemoresistance is a major problem limiting its effectiveness. Thus knowledge of mechanisms underlying this outcome could improve patient prognosis. Here, we report that deletion of a regulatory element in the HOTAIR locus increases glioma cell sensitivity to TMZ and alters transcription of multiple genes. Analysis of a combination of RNA-seq, Capture HiC and patient survival data suggests that CALCOCO1 and ZC3H10 are target genes repressed by the HOTAIR regulatory element and that both function in regulating glioma cell sensitivity to TMZ. Rescue experiments and TAD analysis based on HiC data confirmed this hypothesis. We propose a new regulatory mechanism governing glioma cell TMZ sensitivity.

overall_design: BioProject: PRJNA516515. SRA Study accession:SRP181265 .

first: Lei

last: Zhang

first: Wange

last: Lu